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| | {{STRUCTURE_1x7d| PDB=1x7d | SCENE= }} | | {{STRUCTURE_1x7d| PDB=1x7d | SCENE= }} |
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| - | '''Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine to 1.6 Angstroms'''
| + | ===Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine to 1.6 Angstroms=== |
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| - | ==Overview==
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| - | Ornithine cyclodeaminase catalyzes the conversion of L-ornithine to L-proline by an NAD(+)-dependent hydride transfer reaction that culminates in ammonia elimination. Phylogenetic comparisons of amino acid sequences revealed that the enzyme belongs to the mu-crystallin protein family whose three-dimensional fold has not been reported. Here we describe the crystal structure of ornithine cyclodeaminase in complex with NADH, refined to 1.80 A resolution. The enzyme consists of a homodimeric fold whose subunits comprise two functional regions: (i) a novel substrate-binding domain whose antiparallel beta-strands form a 14-stranded barrel at the oligomeric interface and (ii) a canonical Rossmann fold that interacts with a single dinucleotide positioned for re hydride transfer. The adenosyl moiety of the cofactor resides in a solvent-exposed crevice on the protein surface and makes contact with a "domain-swapped"-like coil-helix module originating from the dyad-related molecule. Diffraction data were also collected to 1.60 A resolution on crystals grown in the presence of l-ornithine. The structure revealed that the substrate carboxyl group interacts with the side chains of Arg45, Lys69, and Arg112. In addition, the ammonia leaving group hydrogen bonds to the side chain of Asp228 and the site of hydride transfer is 3.8 A from C4 of the nicotinamide. The absence of an appropriately positioned water suggested that a previously proposed mechanism that calls for hydrolytic elimination of the imino intermediate must be reconsidered. A more parsimonious description of the chemical mechanism is proposed and discussed in relation to the structure and function of mu-crystallins.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_15518536}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 15518536 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_15518536}} |
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| | ==About this Structure== | | ==About this Structure== |
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| | [[Category: Deaminase]] | | [[Category: Deaminase]] |
| | [[Category: Rossmann fold]] | | [[Category: Rossmann fold]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 14:39:39 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 00:29:47 2008'' |
Revision as of 21:29, 28 July 2008
Template:STRUCTURE 1x7d
Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine to 1.6 Angstroms
Template:ABSTRACT PUBMED 15518536
About this Structure
1X7D is a Single protein structure of sequence from Pseudomonas putida. Full crystallographic information is available from OCA.
Reference
Ornithine cyclodeaminase: structure, mechanism of action, and implications for the mu-crystallin family., Goodman JL, Wang S, Alam S, Ruzicka FJ, Frey PA, Wedekind JE, Biochemistry. 2004 Nov 9;43(44):13883-91. PMID:15518536
Page seeded by OCA on Tue Jul 29 00:29:47 2008
